Phenotype and GWAS Information:

Agronomic Traits

Note: All the agronomic trait is from the article Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Metabolic Traits

Note: All the metabolic trait is from the article Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Some metabolics have two replications, the second replication is end with '_2', like 'mr1002_2'.

Search Results:

The detailed information about mr1441 can be find at here.

GWAS Results:

Note: If the P-value of Linear Regression (LR) or Linear Mixed Model (LMM) ≤ 1e-5 or the rank ≤ 20000, the results are saved. Only the LMM results are plotted below.

Significant Candidate Loci (Lead SNP):

Variation IDVariation ID V6ChromosomePositionLR P-value LMM P-value
vg0222739831 sf0222733962 2 22739831 7.19E-56 4.40E-37
vg0223723973 sf0223718104 2 23723973 8.37E-18 1.35E-07
vg0223663745 sf0223657876 2 23663745 1.54E-15 6.76E-09
vg0223079236 sf0223073367 2 23079236 1.74E-15 3.16E-07
vg0224640486 sf0224634617 2 24640486 7.29E-15 7.93E-06
vg0223556553 sf0223550684 2 23556553 5.48E-14 NA
vg1112606104 sf1112142307 11 12606104 1.15E-13 NA
vg0222897004 sf0222891135 2 22897004 1.26E-11 3.42E-07
vg0224382271 sf0224376402 2 24382271 1.48E-11 4.99E-07
vg0222765370 sf0222759501 2 22765370 1.26E-10 2.79E-07
vg0222683996 sf0222678127 2 22683996 1.63E-08 1.40E-09
vg0131390741 sf0131389697 1 31390741 1.99E-08 NA
vg0222799001 sf0222793132 2 22799001 7.47E-08 1.77E-06
vg1007771968 sf1007787578 10 7771968 9.24E-08 NA